Preface   The United Nations has declared 2014 as Year of Family Farming considering global significance for food and nutrition security. India has enacted a Food Security Act-2013 making access to food a right rather than a subsidized welfare approach. The production target for 2030 is around 480 million tones of food grains as against 240 million tones in 2013. Doubling the production from dwindling land area under agriculture, depleting water sources and quantum and costly energy and labour, the ways and means to reach the target are quite stupendous. One of the options for increased productivity is use of GM crops proven friendly to environment and ecology especially biodiversity. Use of tissue and cell culture for rapid multiplication of economic crops including ornamentals are now well known and demanded by farmers. Micro nutrients and vitamins deficiency in Indian diet lead to anaemia, goiter, myopia, stunted growth and several physiological disorders in skin and body. About 50% of worlds anaemic due to malnutrition are in India. New Life Style diseases like obeisity, diabetes and cardiovascular diseases are also on rise. Biofortified crops like Golden rice rich in iron and tomatoes rich in lycopene are results of recombinant DNA technology. Weedicide tolerant GM soybean and canola resistant to borers are now in farmers field. With climate change and consequent rise in temperature and oceanic currents, natural disasters like drought and flood are rampant. Hurricanes and typhoons devastating standing crops and making agricultural lands unfit for cultivation are threatening Millenium Development Goals (MDG) especially food and nutrition security. The relevance and need for biotechnological interventions are emphasized in this changing scenario of higher demand and lower supply. Biotechnological tools supplement various conventional approaches in conservation, characterization and utlilization for increasing production and productivity of agricultural and horticultural crops. The emerging field of bioinformatics is an integrated field arising from merging of biology and informatics. It is a conglomeration of various new frontiers of science like genomics, proteomics, metabolomics etc. The rich warehouse of proteome and genome information nearly doubling every year, has significant implications and applications in various areas of science including agriculture, horticulture, forestry and food science. Cheminformatics is specialized to a range of problems in the field of chemistry. Chemical pesticide reduction is possible by adopting cheminformatics methods to identify naturally occurring chemical compounds in crops which act against pests. Bioinformatics has transformed the discipline of life science from a purely lab based science to an information science as well. The ICAR has recently launched a National Agricultural Bioinformatics Grid (NABG) to serve as a computational facility in developing national biodatabases and data warehouses. The present book Agriculture Bioinformatics is a compilation of 17 information packed chapters authored by working scientists in the respective discipline. In addition to the theoretical information, practical and applied aspects to boost productivity and quality of crops are given.

Abstract Indian agriculture made a rapid stride, converting the country from food scarcity to sufficiency. But challenges for the Indian agriculture in 21st century are much greater than before. The growing population has to be fed and surplus has to be produced with declining land, water and threat of climate change. Food and livelihood security of increasing population is a cause of concern and has received focused attention across the globe. Food security emphasizes access to sufficient, safe and nutritious food for an active and healthy life. Similarly, livelihood security has the emphasis on income and other resources to enable households to meet their fair needs. The horticulture which includes fruits, vegetables, spices, flowers and medicinal and aromatic plants, has proved beyond doubt its potentiality for gainful diversification. Initiatives taken by Government and other stakeholders have impacted the development in terms of increased production, productivity and availability of horticultural crops. One of the significant developments is that horticulture has moved from rural confine to commercial production and this changing scenario has encouraged private sector investment in production system management. Now the horticulture sector contributes 29.65 per cent to agricultural GDP that has achieved a growth rate of 5-6 per cent during the decade. India has emerged as the second largest producer of fruits and vegetables and has first position in several horticultural crops. Production and export of flowers have increased manifold and the country has a major stake in global trade of spices and cashew nuts. Exports of medicinal plants, fruits and vegetables have also exhibited rising trend.

Abstract Bioinformatics is a discipline combining biology, mathematics and the technology including computational tools and databases. It is one of the fast growing fields in the scientific community. This chapter is intended to provide an overview of the important databases of bioinformatics used for research in molecular biology, taxonomy, conservation biology, forensics and medicine and for the commercial applications in pharmaceutical industry and agricultural biotechnology. This chapter also describes various internet resources available in the field of Bioinformatics. Introduction Bioinformatics has emerged as one of the important scientific disciplines which revolutionized application of life sciences in our day to day life. A simple definition of bioinformatics is: “Bioinformatics is the use of computational techniques for the consolidation and analysis of large scale experimental biological data”. Hence, Bioinformatics has transformed the life science discipline from a purely wet lab-based science to a computationally assisted information science. Application of bioinformatics in life science has multi facets right from gene discovery to drug design where the knowledge on sequence, structure and function of genes and proteins take the lead. The objectives of biological database generation are to: (i) organize the large scale experimental biological data for further investigation, (ii) make the biological data available globally and (iii) avoid duplication of experiments.

Abstract Plant genetic resources constitute the chief component of agro-biodiversity and comprise of land races, modern cultivars and obsolete varieties, breeding lines, genetic stocks and wild species. They provide the basic materials to the plant breeders to utilize genetic variability for the development of high yielding cultivars with a broad genetic base. The utilization of these genetic resources, however, depends upon their efficient and adequate characterization and evaluation, which in turn entails efficient characterization standards and appropriate strategies. Introduction Analysis of trait data generated from characterization and evaluation of the genetic resources is used to understand and use diversity. Currently, a large number of distance measures are available for analyzing similarity/dissimilarity among accessions based on different traits representing different types of variables. The selection of the most appropriate distance measure for each trait is the prerequisite for diversity analysis. One of the approaches is to form clusters where accessions between clusters would be more diverse than the accessions within a cluster. The clustering algorithms require a distance/similarity matrix between the accessions which can be calculated depending upon the nature or type of traits such as morphological and agronomic traits and/or molecular markers.

Abstract Plant Bioinformatics is a new and rapidly evolving field driven by the advances in ‘Omics’ technologies. This chapter is intended to help both beginners and experienced researchers to develop and apply bioinformatics tools to specific areas of plant genomics research. This chapter will also help plant biologists to access and implement comparative genomics studies of the plant genes of interest. Also discussed are the databases which house the data on plant genes and genomes. The chapter ends with a review of basic Perl Programming for sequence motif analysis beneficial for plant biologists. Introduction Ever since the discovery of DNA structure, the field of plant genomics has experienced a dramatic change in the ways scientific problems are approached. With the recent advances in High Throughput analysis clubbed with methods like Physical mapping of genes, RFLP, RAPD, large scale EST sequencing and mRNA protein profiling, there is an enormous amount of biological data available for various analysis. As the amount of data grows tremendously, there is a demand for developing tools and methods to effectively access these assembled data for analysis, modeling, visualization and prediction. In this chapter, we emphasize on some of the key concepts in bioinformatics, tools and databases relevant to plant genomics.

Abstract In recent years there has been a world-wide shift in consumer choice and preferences for herbal drugs. Herbal drugs are crude preparations of various kinds of medicinal plants. It involves dried plant or any part such as leaf, stem, root, flower, or seed. According to WHO survey, about 70-80% of the world population particularly in the developing countries rely on non-conventional medicines mainly of herbal sources for their primary health care.[1] Herbal medicines are being widely accepted for their safety, efficacy, cultural acceptability, better compatibility with the human body and lesser side effects. With the legal acceptance in many countries of the world as an alternative system of medicine, the growth rate of ayurvedic and herbal industry is estimated to be more than 30% for the last 25 years.  Introduction With an ever-increasing global inclination towards the consumption of herbal medicines, there is a growing need of raw materials and to identify the active principles that should be available in optimum quantities at the requisite time. Currently, the herbal medicine sector faces numerous challenges such as narrow genetic base, identification and authentication of species, chemical characterization of active compounds and identification of the target molecules. The pharmacologically active metabolites are produced in very low amounts by the plants and their chemical synthesis is expensive, hence there is a growing pressure of procuring these active metabolites from the wild leading to diminishing the populations, loss of genetic diversity and local extinctions. Domestic cultivation of medicinal plants offers an attractive alternative but not much information is available regarding the cultivation practices for many plants and also, there are issues related to storage practices, quality, safety and stability assessment that need to be addressed. Futher, the study of secondary metabolites and their enhancement is a bottleneck due to lack of knowledge about characterized biosynthetic pathways and enzymes in many plants and how their synthesis is regulated at molecular level. To address these challenges, new molecular tools and biotechnological approaches are much warranted. However, the rapidly changing pace of technology and development of high-throughput research, the field of plant biotechnology is beginning to suffer from data overload. All biotechnological efforts have involved empirical, labor-intensive and time-consuming methods. Bioinformatics is one such approach in which biology and information technology converge. It is an interdisciplinary scientific tool that facilitates both the analysis and integration of information from ‘omics’ technologies including genomics, transcriptomics, proteomics, metabolomics and phenomics. The present chapter highlights some of the important areas in bioinformatics which play a significant role and could also have immense impact in medicinal plants research.

Abstract The completion of large number of genome sequencing projects has generated large volumes of raw sequence data. One of the fundamental tasks in bioinformatics is the creation of databases for data storage and development of tools for analysis. The first plant genome to be completed is that of Arabidopsis thaliana in 2000[49]. This was followed by the rice genome and others. The availability of complete genomes has provided us with an opportunity to analyze them and understand plant biology in a holistic way. It has enhanced our understanding of factors affecting plant growth and development, abiotic and biotic stress, disease resistance, host pathogen interactions amongst others.

Abstract Manipulation of a large number of genes is often required for the improvement of even the simplest character. Molecular marker trace valuable alleles in a segregating population and mapping them. Genome mapping has emerged as a powerful new approach for research in botany, agriculture and other related fields. Genome mapping methods help to locate specific DNA markers to delineate when one has reached particular gene of interest and forming a molecular map. DNA mapping encompasses a wide range of techniques useful for studying DNA at different levels of magnification. Genetic Linkage Mapping Using Molecular Markers, Development of Genetic Maps, Mapping populations and comparative genomics are elucidated. Introduction Understanding biology and genetics at molecular level has become very important for better understanding and manipulation of genome architecture. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways including genetic fingerprinting, identification of duplicates and selecting core collections, determination of genetic distances, genome analysis, identification of markers associated with desirable breeding traits which are useful in marker assisted breeding, genomics and development of transgenics. Use of these markers also significantly reduce breeding time and cycles required for crop improvement. Molecular level understanding of the inheritance of agriculturally important traits creates new opportunities to streamline plant breeding.

Abstract Development of reliable automated techniques for the identification and annotation of exon and intron regions in a gene has been an important area of research in the field of computational biology. Several classical approaches like probabilistic model, artificial intelligence and digital signal processing are already in use to cater to this challenging task. In this work, we propose a Support Vector Machine based kernel learning approach for detecting splice site patterns and their conservation across the species. Electron-Ion Interaction Potential (EIIP) values of nucleotides were used to map DNA character sequences to corresponding numeric sequences. Radial Basis Function (RBF) SVM kernel was trained with cross validation using these EIIP numeric sequences. This was then tested on test gene datasets of multiple species for detection of splice site pattern. Receiver Operating Characteristic (ROC) curves and various other statistical measures have been utilized for displaying the performance of the classifier. Results indicate an inter-species splice site conversion profile.

Abstract Support Vector Machine (SVM) is a classification and regression prediction tool, widely employed in different fields of science and engineering. A review on some recent plant bioinformatics applications using SVM is made. Different soft wares for SVM are also explained. There is a growing amount of plant genomes data currently available from different sources. Recent advances made using SVM and Feature selection in plant bioinformatics are reviewed Introduction Recent developments in genomic and post-genomic research have generated a vast amount of biological data. This data is growing exponentially with the advancement of research technologies. Several plant genomes have been sequenced recently. For instance, the complete sequence of Arabidopsis thaliana and the draft sequence of rice are now available[1]. Also, sequencing of several other plants including maize, tomato, sorghum, etc is in progress. Considering the amount and complexity of this data, it is impossible for an expert to analyze and compare the data manually. Thus, there is an increasing need for computational methods that can efficiently store, organize and interpret this large amount of data.

Abstract The field of bioinformatics emerged as a tool to facilitate biological discoveries more than 10 years ago. The ability to capture, manage, process, analyze and interpret data became more important than ever. Bioinformatics in agricultural science has many complex aspects and problems that must be resolved due to the involvement of a wide variety of fields and subjects. Consequently, the establishment of interdisciplinary research areas is required, which should include collaboration among experimental and informatics researchers in different fields within industry, academia, and government. Thus, the Agricultural Bioinformatics Special Interest Group was established to promote interaction among researchers and provide an opportunity to report on bioinformatics studies in agricultural science: design and analysis of functional foods, scientific testing of food safety, breeding of agricultural organisms, development of environmental friendly agricultural chemicals, bioremediation and production of useful chemical materials using microorganisms, measuring and monitoring biodiversity, statistical genetics in resource ecology, and so on. The activities of the Agricultural Bioinformatics Special Interest Group include (1) Studies of applied bioinformatics in the agricultural science (2) Development of new research areas in agricultural science using bioinformatics (3) Practical application of bioinformatics technologies in the field of agricultural science (4) Development of new bioinformatics technologies characteristic of agricultural science.

Abstract Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression, mechanism of evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mitochondrial gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms. This evolutionary episode has significant contribution among animals as well as plants and serves as an important genomic evolutionary event for the analysis of mitogenomes on large scale.

Abstract Spices are aromatic substances of plant origin which are commonly used for flavouring, seasoning and imparting aroma in foodstuffs. They are cultivated in an area of 5.98 million ha globally with a total production of 7.31 million tons. India is considered as the home of majority of these spices from ancient times and sizable area of the country is under spice cultivation. The latest statistics shows that the total cultivated area in India under spices is 2.89 million ha with a total production of 3.33 million tonnes. About 109 plants belonging to 31 families are recognized as spices useful as ingredients in food. Many of them have been demonstrated to mediate therapeutic benefits for wide spectra of diseases ranging from multiple sclerosis to colorectal cancer. Introduction Advances in molecular genetics in the last 20 years like rapid DNA amplification techniques using PCR, rapid sequencing methods and computational software programs have enabled the placement of molecular markers on to the maps of chromosomes of most major crop species and the subsequent tagging of genes of interest by their placement near those markers[38]. Unfortunately very little or scanty molecular data of spices are available in the public domain (Table 12.1). ‘Orphan crops’ like spices which have not yet received the investment of research effort or funding can exploit comparative genomics and bioinformatics to assist research and crop improvement provided they are related to a well-characterized model plant species.

Abstract The study of palm genomics can aid to understand the genetic and molecular knowhow of all biological processes in palms that are vital tothe palm species. This knowledge will allow the path for the fruitful exploitation of palms as biological resources in the development of new cultivars of improved quality and with shortened economic and environmental costs. This knowledge is also vital for the development of new diagnostic tools. Traits considered of primary interest are resistance to pathogens and abiotic stress, fruit quality and yield. Genomics and bioinformatics approaches helped in unraveling the genomes of economicpalsm like coconut, oilpalm and datepalm. The genome characteristics and tools for genome analysis are provided in the chapter. Due to the economic importance of cocoa, many scientific research studies (genome, EST, transcriptome) have been carried out in the past years in this crop also. Introduction Plantation crops constitute a large group of crops. The major plantation crops include coconut, arecanut, oil palm, cashew, tea, coffee and rubber; and the minor plantation crops include cocoa (Prapulla and Indira, 2014). India is the third largest producer of coconut and goes in front of the ninety coconut-producing countries of the world (Richard 2013). India is the largest producer and consumer of cashew nuts (Mohod et al., 2011.). India also occupies number one position in arecanut production (Dwivedi et al.,2008) besides being the largest tea producers in the world. While Coffee is the second largest traded commodity in the world, it has, in recent times become an extremely important foreign exchange (Prapulla and Indira, 2014).

Abstract Microorganisms constituting the major fraction of the total biomass, are the main source of biodiversity in our planet and play an essential role in maintaining biogeochemical processes, which ultimately regulate the functioning of the Biosphere. Molecular ecological studies of microbial communities revealed that only a small fraction of total microbes in nature have been identified and characterized so far, since the majority of them are recalcitrant to cultivation. The emergence of ‘metagenomics’ have paved ways to the analysis and understanding of the genetic diversity, population structure, and ecology of complex microbial assemblages through culture – independent genomics-based approaches. The concept, metagenome, represents the total microbial genome in natural ecosystem consisting of genomes from both culturable microorganisms and viable but nonculturable bacteria. The construction and screening of metagenomic libraries in culturable bacteria constitute a valuable resource for obtaining novel microbial genes and products. Several novel enzymes and antibiotics have been identified through the metagenomic approach from many different microbial communities. This technology in the near future will provide breakthrough advances in the field of medicine, agriculture, energy production and bioremediation. This paper looks in to the various steps involved in metagenomic studies and how its potential can be utilized in the various aspects of agriculture to improve crop production and protection. The importance and role of bioinformatics in deciphering metagenomic data are also looked into.

Abstract Our biological heritage, from genes to ecosystems, is threatened on a global scale. Biological species, the prime focus on biodiversity, provide all our basic requirements such as food, medicine, fuel and things for well being, make nature’s sustainability through purifying air and water, pollinating crops, etc. and motivate us at a deep emotional level. During the course of human civilization and consequent urbanization process biological species and environment have been degraded. It is estimated that about 20% of all species are expected to be lost within 30 years and 50% or more by the end of the 21st century [36]. The current rates of species extinction are 1000–10,000 times higher than the background rate of 10-7 species per year inferred from fossil record. Today, we seem to be losing two to five species per hour from tropical forests alone. This amounts to a loss of 16 m population per year or 1800 populations per hour. This led to biodiversity crisis in the global level [23,26,35] and generated an outpouring of research on biodiversity for the last 25 years. As a result we could have a general understanding about the distribution of biodiversity, the proximate causes (habitat loss, habitat fragmentation, habitat degradation, invasive species, pollution, resource exploitation) contributing to its loss, sketches of the root causes of biodiversity loss, and the outlines of better management policies. Since the establishment of the convention on biological diversity in 1992, conservation of biodiversity has become a priority concern on the international agenda.

Abstract There has been consistent narrowing down of gap in our knowledge about various ‘omics’ as the omics’ based disciplines are filled with valuable information emerging from research. During the last two decades, the practice of genetics has not only changed the broad horizons of medicine but also found its niche through “high-dimensional biology” there by allowing geneticists to reframe the good-old definition of gene from a locatable region of genome sequence involved in heritability to a locatable region of genome sequence associated with a functional region or a functor. Various other scientists viewed genetics ‘‘as the study of single genes and their effects’’ and genomics as ‘‘the study not just of single genes, but of the functions and interactions of all the genes in the genome.’’ We will cover the qualitative difference that bridges various disciplines casing Omics.

Abstract Advances in genome sequencing technologies have made it possible to uncover the whole genome sequences of numerous organisms from microbes to higher eukaryotes. Haemophilus influenza, a free living bacterium, was the first complete genome to be sequenced in 1995 by a team headed by J. Craig Venter and Hamilton Smith at The Institute for Genomic Research (TIGR). Immediately after this, Mycoplasma genitalium, a bacterium responsible for reproductive-tract infections and well-known for having the shortest genome of all free-living organisms was sequenced. Subsequently, TIGR unearthed the genome sequences of many microbes like Methanococcus jannaschii, Archaeoglobus fulgidus, Helicobacter pylori, Borrelia burgdorferi etc. During the years 1996-2000, the complete genome sequences of several model organisms such as bacterium Escherichia coli K-12, baker’s yeast Saccharomyces cerevisiae, nematode Caenorhabditis elegans, fruit fly Drosophila melanogaster etc were published. Since then the complete genome sequences of many other eukaryotes have been released by the genome sequencing community.

A A.thaliana 192 AAT 376 AATAAA hexamer 374 Ab initio Approaches 108 Ab initio Gene-finders 377 Ab initio structure prediction 234 ABC transporters 135 ABRC 95 Abstract Syntax Notation 1 (ASN.1) 37 Ac/Ds tag line 95 ACC deaminase 300 ACD/ChemSketch 137 AceDB 361 Acidobacteria 301, 307 Acronychia pedunculata 139 Acronycine 139 Active X 252 ADDA 30 Aadenine 340 Advanced Visual Systems 252 Aegle marmelos 139 AFLPs 60, 273, 351 Agarase 297 AgBase 80, 110 Aging-related research 347 Agricultural biotechnology 9 Agricultural GDP 2 Agriculturally important traits 156 AGRIS 95 Agro-biodiversity 51 Agro-technique 92 Agrobacterium tumefaciens 304